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Structure paper

TitleStructural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication.
Journal, issue, pagesJ. Am. Chem. Soc., Vol. 144, Page 8054-8065, Year 2022
Publish dateSep 21, 2021 (structure data deposition date)
AuthorsRyan, B.J. / Yang, H. / Bacurio, J.H.T. / Smith, M.R. / Basu, A.K. / Greenberg, M.M. / Freudenthal, B.D.
External linksJ. Am. Chem. Soc. / PubMed:35499923
MethodsX-ray diffraction
Resolution1.71 - 2.31 Å
Structure data

PDB-7s9j:
Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dC
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

PDB-7s9k:
Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dA
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-7s9l:
Crystal Structure of DNA Polymerase Beta with Ring open intermediate Fapy-dG base-paired with a dC
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-7s9m:
Crystal Structure of DNA Polymerase Beta with Ring open intermediate Fapy-dG base-paired with a dA
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-7s9n:
Binary complex of DNA Polymerase Beta with Fapy-dG in the template position
Method: X-RAY DIFFRACTION / Resolution: 1.71 Å

PDB-7s9o:
Binary complex of DNA Polymerase Beta with Ring open Intermediate Fapy-dG in the template position
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-7s9p:
Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-7s9q:
Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dATP analog
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-SO4:
SULFATE ION

ChemComp-XC5:
2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine

ChemComp-MN:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-F2A:
2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsDNA BNDING PROTEIN/DNA / Fapy-dG / duplex DNA / polymerase Beta / non-mutagenic / DNA BNDING PROTEIN-DNA complex / DNA BINDING PROTEIN/DNA / mismatch / DNA BINDING PROTEIN-DNA complex / DNA BINDING/DNA / DNA BINDING-DNA complex / binary / Fapy-dG Intermediate / mutagenic

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